Software Cartography: Thematic Software Visualization with Consistent Layout

Software visualizations can provide a concise overview of a complex software system. Unfortunately, as software has no physical shape, there is no `natural' mapping of software to a two-dimensional space. As a consequence most visualizations tend to use a layout in which position and distance have no meaning, and consequently layout typically diverges from one visualization to another. We propose an approach to consistent layout for software visualization, called Software Cartography, in which the position of a software artifact reflects its vocabulary, and distance corresponds to similarity of vocabulary. We use Latent Semantic Indexing (LSI) to map software artifacts to a vector space, and then use Multidimensional Scaling (MDS) to map this vector space down to two dimensions. The resulting consistent layout allows us to develop a variety of thematic software maps that express very different aspects of software while making it easy to compare them. The approach is especially suitable for comparing views of evolving software, as the vocabulary of software artifacts tends to be stable over time. We present a prototype implementation of Software Cartography, and illustrate its use with practical examples from numerous open-source case studies.

Patient satisfaction with primary care: an observational study comparing anthroposophic and conventional care

BACKGROUND: This study is part of a cross-sectional evaluation of complementary medicine providers in primary care in Switzerland. It compares patient satisfaction with anthroposophic medicine (AM) and conventional medicine (CON). METHODS: We collected baseline data on structural characteristics of the physicians and their practices and health status and demographics of the patients. Four weeks later patients assessed their satisfaction with the received treatment (five items, four point rating scale) and evaluated the praxis care (validated 23-item questionnaire, five point rating scale). 1946 adult patients of 71 CON and 32 AM primary care physicians participated. RESULTS: 1. Baseline characteristics: AM patients were more likely female (75.6% vs. 59.0%, p < 0.001) and had higher education (38.6% vs. 24.7%, p < 0.001). They suffered more often from chronic illnesses (52.8% vs. 46.2%, p = 0.015) and cancer (7.4% vs. 1.1%). AM consultations lasted on average 23,3 minutes (CON: 16,8 minutes, p < 0.001). 2. Satisfaction: More AM patients expressed a general treatment satisfaction (56.1% vs. 43.4%, p < 0.001) and saw their expectations completely fulfilled at follow-up (38.7% vs. 32.6%, p < 0.001). AM patients reported significantly fewer adverse side effects (9.3% vs. 15.4%, p = 0.003), and more other positive effects from treatment (31.7% vs. 17.1%, p < 0.001). Europep: AM patients appreciated that their physicians listened to them (80.0% vs. 67.1%, p < 0.001), spent more time (76.5% vs. 61.7%, p < 0.001), had more interest in their personal situation (74.6% vs. 60.3%, p < 0.001), involved them more in decisions about their medical care (67.8% vs. 58.4%, p = 0.022), and made it easy to tell the physician about their problems (71.6% vs. 62.9%, p = 0.023). AM patients gave significantly better rating as to information and support (in 3 of 4 items p [less than or equal to] 0.044) and for thoroughness (70.4% vs. 56.5%, p < 0.001). CONCLUSION: AM patients were significantly more satisfied and rated their physicians as valuable partners in the treatment. This suggests that subject to certain limitations, AM therapy may be beneficial in primary care. To confirm this, more detailed qualitative studies would be necessary.

Consistent Layout for Thematic Software Maps

Software visualizations can provide a concise overview of a complex software system. Unfortunately, since software has no physical shape, there is no “natural“ mapping of software to a two-dimensional space. As a consequence most visualizations tend to use a layout in which position and distance have no meaning, and consequently layout typical diverges from one visualization to another. We propose a consistent layout for software maps in which the position of a software artifact reflects its \emph{vocabulary}, and distance corresponds to similarity of vocabulary. We use Latent Semantic Indexing (LSI) to map software artifacts to a vector space, and then use Multidimensional Scaling (MDS) to map this vector space down to two dimensions. The resulting consistent layout allows us to develop a variety of thematic software maps that express very different aspects of software while making it easy to compare them. The approach is especially suitable for comparing views of evolving software, since the vocabulary of software artifacts tends to be stable over time.

MorphoGraphX: A platform for quantifying morphogenesis in 4D

Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX (www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software’s modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.DOI: http://dx.doi.org/10.7554/eLife.05864.001Author keywordsResearch organism

Irrigation of continent catheterizable ileal pouches: tap water can replace sterile solutions because it is safe, easy, and economical

Continent catheterizable ileal pouches require regular irrigations to reduce the risk of bacteriuria and urinary tract infections (UTIs).

Percutaneous closure of the patent foramen ovale, easy does it.

Closure of the patent foramen ovale does not benefit from echocardiographic guidance in the majority of cases. Guiding these procedures with fluoroscopy only reduces procedure time, radiation exposure, and amount of contrast medium. There is a clear trend to abandon echocardiographic guidance for this procedure over time and with growing experience.

Feasibility and acceptance of electronic quality of life assessment in general practice: an implementation study

Background Patients' health related quality of life (HRQoL) has rarely been systematically monitored in general practice. Electronic tools and practice training might facilitate the routine application of HRQoL questionnaires. Thorough piloting of innovative procedures is strongly recommended before the conduction of large-scale studies. Therefore, we aimed to assess i) the feasibility and acceptance of HRQoL assessment using tablet computers in general practice, ii) the perceived practical utility of HRQoL results and iii) to identify possible barriers hindering wider application of this approach. Methods Two HRQoL questionnaires (St. George's Respiratory Questionnaire SGRQ and EORTC QLQ-C30) were electronically presented on portable tablet computers. Wireless network (WLAN) integration into practice computer systems of 14 German general practices with varying infrastructure allowed automatic data exchange and the generation of a printout or a PDF file. General practitioners (GPs) and practice assistants were trained in a 1-hour course, after which they could invite patients with chronic diseases to fill in the electronic questionnaire during their waiting time. We surveyed patients, practice assistants and GPs regarding their acceptance of this tool in semi-structured telephone interviews. The number of assessments, HRQoL results and interview responses were analysed using quantitative and qualitative methods. Results Over the course of 1 year, 523 patients filled in the electronic questionnaires (1–5 times; 664 total assessments). On average, results showed specific HRQoL impairments, e.g. with respect to fatigue, pain and sleep disturbances. The number of electronic assessments varied substantially between practices. A total of 280 patients, 27 practice assistants and 17 GPs participated in the telephone interviews. Almost all GPs (16/17 = 94%; 95% CI = 73–99%), most practice assistants (19/27 = 70%; 95% CI = 50–86%) and the majority of patients (240/280 = 86%; 95% CI = 82–91%) indicated that they would welcome the use of electronic HRQoL questionnaires in the future. GPs mentioned availability of local health services (e.g. supportive, physiotherapy) (mean: 9.4 ± 1.0 SD; scale: 1 – 10), sufficient extra time (8.9 ± 1.5) and easy interpretation of HRQoL results (8.6 ± 1.6) as the most important prerequisites for their use. They believed HRQoL assessment facilitated both communication and follow up of patients' conditions. Practice assistants emphasised that this process demonstrated an extra commitment to patient centred care; patients viewed it as a tool, which contributed to the physicians' understanding of their personal condition and circumstances. Conclusion This pilot study indicates that electronic HRQoL assessment is technically feasible in general practices. It can provide clinically significant information, which can either be used in the consultation for routine care, or for research purposes. While GPs, practice assistants and patients were generally positive about the electronic procedure, several barriers (e.g. practices' lack of time and routine in HRQoL assessment) need to be overcome to enable broader application of electronic questionnaires in every day medical practice.